The skull of the unknown man was taken from Tasmania in the 1830s and had been held by the University of Aberdeen since the early 1850s.
It is understood he was part of the Big River tribe and was shot at Shannon River in the island state’s Central Highlands.
Tasmanian Aboriginal Centre’s Andry Sculthorpe and elder Jeanette James arrived in Hobart with the remains on Thursday.
They also brought back a shell necklace, made by a woman on a Bass Strait island in the 1880s, from the University of Glasgow’s Hunterian Museum.